addImageTracks	HiTC-internal
as.list,HTClist-method	HTClist-class
binningC	binningC
c,HTCexp-method	HTCexp-class
c,HTClist-method	HTClist-class
colorC	HiTC-internal
CQC	CQC
detail	HTCexp-class
detail,HTCexp-method	HTCexp-class
detail,HTClist-method	HTClist-class
detail-methods	HTCexp-class
directionalityIndex	directionalityIndex
discretize	discretize
divide	HTCexp-class
divide,HTCexp,HTCexp-method	HTCexp-class
divide-methods	HTCexp-class
E14	Nora_5C
export-defunct	HTCexp-class
export.my5C	export.my5C
exportC	exportC
extractRegion	extractRegion
forcePairwise	HTClist-class
forcePairwise,HTClist-method	HTClist-class
forceSymmetric,HTCexp,character-method	HTCexp-class
forceSymmetric,HTCexp,missing-method	HTCexp-class
forceSymmetric,HTClist,character-method	HTClist-class
forceSymmetric,HTClist,missing-method	HTClist-class
forceTriangular	HTCexp-class
forceTriangular,HTCexp-method	HTCexp-class
forceTriangular-method	HTCexp-class
gdiag	HiTC-internal
getAnnotatedRestrictionSites	getAnnotatedRestrictionSites
getCombinedContacts	HTClist-class
getCombinedContacts,HTClist-method	HTClist-class
getCombinedContacts-method	HTClist-class
getCombinedIntervals	HTClist-class
getCombinedIntervals,HTClist-method	HTClist-class
getCombinedIntervals-method	HTClist-class
getData2Map	HiTC-internal
getDeltaRange	HiTC-internal
getExpectedCounts	getExpectedCounts
getPearsonMap	getPearsonMap
getRestrictionFragmentsPerChromosome	getRestrictionFragmentsPerChromosome
heatmapC	HiTC-internal
HTCexp	HTCexp-class
HTCexp-class	HTCexp-class
HTClist	HTClist-class
HTClist-class	HTClist-class
id	HTCexp-class
id,GRanges-method	HTCexp-class
id-methods	HTCexp-class
import.my5C	import.my5C
importC	importC
intdata	HTCexp-class
intdata,HTCexp-method	HTCexp-class
intdata-method	HTCexp-class
intdata<-	HTCexp-class
intdata<-,HTCexp,Matrix-method	HTCexp-class
intdata<--methods	HTCexp-class
intervalsDist	intervalsDist
isBinned	HTCexp-class
isBinned,HTCexp-method	HTCexp-class
isBinned,HTClist-method	HTClist-class
isBinned-methods	HTCexp-class
isComplete	HTClist-class
isComplete,HTClist-method	HTClist-class
isComplete-methods	HTClist-class
isIntraChrom	HTCexp-class
isIntraChrom,HTCexp-method	HTCexp-class
isIntraChrom,HTClist-method	HTClist-class
isIntraChrom-methods	HTCexp-class
isPairwise	HTClist-class
isPairwise,HTClist-method	HTClist-class
isPairwise-method	HTClist-class
isSymmetric	HTCexp-class
isSymmetric,HTCexp-method	HTCexp-class
isSymmetric-methods	HTCexp-class
isTriangular,HTCexp-method	HTCexp-class
isTriangular-methods	HTCexp-class
mapC	mapC
mapC,HTCexp,ANY-method	mapC
mapC,HTCexp,HTCexp-method	mapC
mapC,HTClist,ANY-method	mapC
mapC-methods	mapC
MEF	Nora_5C
my5C2gr	HiTC-internal
Nora_5C	Nora_5C
normICE	normICE
normLGF	normLGF
normPerExpected	HTCexp-class
normPerExpected,HTCexp-method	HTCexp-class
normPerExpected,HTClist-method	HTClist-class
normPerExpected-methods	HTCexp-class
normPerReads	HTCexp-class
normPerReads,HTCexp-method	HTCexp-class
normPerReads-methods	HTCexp-class
normPerTrans	HTCexp-class
normPerTrans,HTCexp,HTCexp,HTCexp-method	HTCexp-class
normPerTrans-methods	HTCexp-class
normPerZscore-defunct	HTCexp-class
pair.chrom	HiTC-internal
pca.hic	pca.hic
plot,HTCexp,ANY-method	HTCexp-class
plot,HTCexp,HTCexp-method	HTCexp-class
plot,HTClist,ANY-method	HTClist-class
range	HTCexp-class
range,HTCexp-method	HTCexp-class
range,HTClist-method	HTClist-class
range-method	HTCexp-class
ranges	HTClist-class
ranges,HTClist-method	HTClist-class
ranges-methods	HTClist-class
reduce	HTClist-class
reduce,HTClist-method	HTClist-class
reduce-methods	HTClist-class
removeIntervals	removeIntervals
seqlevels	HTCexp-class
seqlevels,HTCexp-method	HTCexp-class
seqlevels,HTClist-method	HTClist-class
seqlevels-method	HTCexp-class
seq_name-deprecated	HTCexp-class
setGenomicFeatures	setGenomicFeatures
setIntervalScale	setIntervalScale
show,HTCexp-method	HTCexp-class
show,HTClist-method	HTClist-class
substract	HTCexp-class
substract,HTCexp,HTCexp-method	HTCexp-class
substract-methods	HTCexp-class
summary,HTCexp-method	HTCexp-class
summary,HTClist-method	HTClist-class
tricube	HiTC-internal
triViewC	HiTC-internal
xy_intervals	HTCexp-class
xy_intervals,HTCexp-method	HTCexp-class
xy_intervals-methods	HTCexp-class
x_intervals	HTCexp-class
x_intervals,HTCexp-method	HTCexp-class
x_intervals-methods	HTCexp-class
x_intervals<-	HTCexp-class
x_intervals<-,HTCexp,GRanges-method	HTCexp-class
x_intervals<--methods	HTCexp-class
y_intervals	HTCexp-class
y_intervals,HTCexp-method	HTCexp-class
y_intervals-methods	HTCexp-class
y_intervals<-	HTCexp-class
y_intervals<-,HTCexp,GRanges-method	HTCexp-class
y_intervals<--methods	HTCexp-class
[,HTClist,ANY,ANY,ANY-method	HTClist-class
[,HTClist,ANY,ANY-method	HTClist-class
